int main(int argc, char **argv) { AjPSeqall seqall; AjPSeq seq = NULL; AjPFile outf = NULL; AjPStr strand = NULL; AjPStr substr = NULL; AjPStr bases = NULL; ajint begin; ajint end; ajint len; ajint minlen; float minobsexp; float minpc; ajint window; ajint shift; ajint plotstart; ajint plotend; float *xypc = NULL; float *obsexp = NULL; AjBool *thresh = NULL; float obsexpmax; ajint i; ajint maxarr; embInit("newcpgreport",argc,argv); seqall = ajAcdGetSeqall("sequence"); window = ajAcdGetInt("window"); shift = ajAcdGetInt("shift"); outf = ajAcdGetOutfile("outfile"); minobsexp = ajAcdGetFloat("minoe"); minlen = ajAcdGetInt("minlen"); minpc = ajAcdGetFloat("minpc"); substr = ajStrNew(); bases = ajStrNewC("CG"); maxarr = 0; while(ajSeqallNext(seqall, &seq)) { begin = ajSeqallGetseqBegin(seqall); end = ajSeqallGetseqEnd(seqall); strand = ajSeqGetSeqCopyS(seq); ajStrFmtUpper(&strand); ajStrAssignSubC(&substr,ajStrGetPtr(strand),--begin,--end); len=ajStrGetLen(substr); if(len > maxarr) { AJCRESIZE(obsexp, len); AJCRESIZE(thresh, len); AJCRESIZE(xypc, len); maxarr = len; } for(i=0;i<len;++i) obsexp[i]=xypc[i]=0.0; newcpgreport_findbases(substr, len, window, shift, obsexp, xypc, bases, &obsexpmax, &plotstart, &plotend); newcpgreport_identify(outf, obsexp, xypc, thresh, 0, len, shift, ajStrGetPtr(bases), ajSeqGetNameC(seq), minlen, minobsexp, minpc, ajStrGetPtr(strand)); ajStrDel(&strand); } ajStrDel(&bases); ajSeqDel(&seq); ajStrDel(&substr); ajFileClose(&outf); AJFREE(obsexp); AJFREE(thresh); AJFREE(xypc); ajSeqallDel(&seqall); embExit(); return 0; }
int main(int argc, char **argv) { AjPSeqall seqall; AjPSeq seq = NULL; AjPReport outf = NULL; AjPFile inf = NULL; ajint begin; ajint end; AjPList l = NULL; AjPStr strand = NULL; AjPStr substr = NULL; AjPStr line = NULL; AjPStr name = NULL; AjPStr acc = NULL; AjPStr bf = NULL; AjPStr menu; AjPStr pattern = NULL; AjPStr opattern = NULL; AjPStr pname = NULL; AjPStr key = NULL; AjPStr value = NULL; AjPTable atable = NULL; AjPTable btable = NULL; ajint mismatch; ajint minlength; ajint sum; ajint v; char cp; const char *p; embInit("tfscan", argc, argv); seqall = ajAcdGetSeqall("sequence"); outf = ajAcdGetReport("outfile"); mismatch = ajAcdGetInt("mismatch"); minlength = ajAcdGetInt("minlength"); menu = ajAcdGetListSingle("menu"); pname = ajStrNew(); cp=ajStrGetCharFirst(menu); if(cp=='F') ajStrAssignC(&pname,"tffungi"); else if(cp=='I') ajStrAssignC(&pname,"tfinsect"); else if(cp=='O') ajStrAssignC(&pname,"tfother"); else if(cp=='P') ajStrAssignC(&pname,"tfplant"); else if(cp=='V') ajStrAssignC(&pname,"tfvertebrate"); else if(cp=='C') inf = ajAcdGetDatafile("custom"); if(cp!='C') { inf = ajDatafileNewInNameS(pname); if(!inf) ajFatal("Either EMBOSS_DATA undefined or TFEXTRACT needs running"); } name = ajStrNew(); acc = ajStrNew(); bf = ajStrNewC(""); substr = ajStrNew(); line = ajStrNew(); pattern = ajStrNewC("AA"); opattern = ajStrNew(); while(ajSeqallNext(seqall, &seq)) { begin=ajSeqallGetseqBegin(seqall); end=ajSeqallGetseqEnd(seqall); ajStrAssignC(&name,ajSeqGetNameC(seq)); strand=ajSeqGetSeqCopyS(seq); ajStrAssignSubC(&substr,ajStrGetPtr(strand),begin-1,end-1); ajStrFmtUpper(&substr); l=ajListNew(); atable = ajTablestrNew(1000); btable = ajTablestrNew(1000); sum=0; while(ajReadlineTrim(inf,&line)) { p = ajStrGetPtr(line); if(!*p || *p=='#' || *p=='\n' || *p=='!') continue; ajFmtScanS(line,"%S%S%S",&pname,&pattern,&acc); p += ajStrGetLen(pname); while(*p && *p==' ') ++p; p += ajStrGetLen(pattern); while(*p && *p==' ') ++p; p += ajStrGetLen(acc); while(*p && *p==' ') ++p; ajStrAssignS(&opattern,pattern); ajStrAssignC(&bf,p); /* rest of line */ v = embPatVariablePattern(pattern,substr,pname,l,0, mismatch,begin); if(v) { key = ajStrNewS(pname); value = ajStrNewS(acc); ajTablePut(atable,(void *)key,(void *)value); key = ajStrNewS(pname); value = ajStrNewS(bf); ajTablePut(btable,(void *)key,(void *)value); } sum += v; } if(sum) tfscan_print_hits(&l,sum,outf,atable,seq,minlength, btable); ajFileSeek(inf,0L,0); ajListFree(&l); ajTablestrFree(&atable); ajTablestrFree(&btable); ajStrDel(&strand); } ajStrDel(&line); ajStrDel(&name); ajStrDel(&acc); ajStrDel(&pname); ajStrDel(&opattern); ajStrDel(&bf); ajStrDel(&pattern); ajStrDel(&substr); ajSeqDel(&seq); ajFileClose(&inf); ajReportClose(outf); ajReportDel(&outf); ajSeqallDel(&seqall); ajSeqDel(&seq); ajStrDel(&menu); embExit(); return 0; }
int main(int argc, char **argv) { AjPFile inf = NULL; AjPFile inf2 = NULL; AjPFeattable tab = NULL; AjPReport report = NULL; AjPSeq sequence = NULL; AjPStr redatanew = NULL; AjPStr str = NULL; AjPStr regexp = NULL; AjPStr temp = NULL; AjPStr text = NULL; AjPStr docdata = NULL; AjPStr data = NULL; AjPStr accession = NULL; AjPStr name = NULL; EmbPPatMatch match = NULL; AjPStr savereg = NULL; AjPStr fthit = NULL; AjBool full; AjBool prune; ajint i; ajint number; ajint start; ajint end; ajint length; ajint zstart; ajint zend; const char *p; ajint seqlength; AjPStr tmpstr = NULL; AjPStr tailstr = NULL; AjPFeature gf; embInit("patmatmotifs", argc, argv); ajStrAssignC(&fthit, "SO:0001067"); savereg = ajStrNew(); str = ajStrNew(); regexp = ajStrNew(); temp = ajStrNew(); data = ajStrNew(); accession = ajStrNew(); text = ajStrNew(); name = ajStrNew(); sequence = ajAcdGetSeq("sequence"); report = ajAcdGetReport("outfile"); full = ajAcdGetBoolean("full"); prune = ajAcdGetBoolean("prune"); ajSeqFmtUpper(sequence); /* prosite regexs are all upper case */ tab = ajFeattableNewSeq(sequence); ajStrAssignC(&tailstr, ""); seqlength = ajStrGetLen(str); str = ajSeqGetSeqCopyS(sequence); redatanew = ajStrNewC("PROSITE/prosite.lines"); docdata = ajStrNewC("PROSITE/"); inf = ajDatafileNewInNameS(redatanew); if(!inf) ajFatal("Either EMBOSS_DATA undefined or PROSEXTRACT needs running"); ajFmtPrintAppS(&tmpstr, "Full: %B\n", full); ajFmtPrintAppS(&tmpstr, "Prune: %B\n", prune); ajFmtPrintAppS(&tmpstr, "Data_file: %F\n", inf); ajReportSetHeaderS(report, tmpstr); while(ajReadlineTrim(inf, ®exp)) { p=ajStrGetPtr(regexp); if(*p && *p!=' ' && *p!='^') { p=ajSysFuncStrtok(p," "); ajStrAssignC(&name,p); if(prune) if(ajStrMatchCaseC(name,"myristyl") || ajStrMatchCaseC(name,"asn_glycosylation") || ajStrMatchCaseC(name,"camp_phospho_site") || ajStrMatchCaseC(name,"pkc_phospho_site") || ajStrMatchCaseC(name,"ck2_phospho_site") || ajStrMatchCaseC(name,"tyr_phospho_site")) { for(i=0;i<4;++i) ajReadlineTrim(inf, ®exp); continue; } p=ajSysFuncStrtok(NULL," "); ajStrAssignC(&accession,p); } if(ajStrPrefixC(regexp, "^")) { p = ajStrGetPtr(regexp); ajStrAssignC(&temp,p+1); ajStrAssignC(&savereg,p+1); match = embPatMatchFind(temp, str, ajFalse, ajFalse); number = embPatMatchGetNumber(match); for(i=0; i<number; i++) { seqlength = ajStrGetLen(str); start = 1+embPatMatchGetStart(match, i); end = 1+embPatMatchGetEnd(match, i); length = embPatMatchGetLen(match, i); gf = ajFeatNew(tab, NULL, fthit, start, end, (float) length, ' ', 0); ajFmtPrintS(&tmpstr, "*motif %S", name); ajFeatTagAddSS(gf, NULL, tmpstr); if(start-5<0) zstart = 0; else zstart = start-5; if(end+5> seqlength) zend = end; else zend = end+5; ajStrAssignSubS(&temp, str, zstart, zend); } if(full && number) { ajStrAssignC(&redatanew,ajStrGetPtr(docdata)); ajStrAppendC(&redatanew,ajStrGetPtr(accession)); inf2 = ajDatafileNewInNameS(redatanew); if(!inf2) continue; /* ** Insert Prosite documentation from files made by ** prosextract.c */ ajFmtPrintAppS(&tailstr, "Motif: %S\n", name); ajFmtPrintAppS(&tailstr, "Count: %d\n\n", number); while(ajReadlineTrim(inf2, &text)) ajFmtPrintAppS(&tailstr, "%S\n", text); ajFmtPrintAppS(&tailstr, "\n***************\n\n"); ajFileClose(&inf2); } embPatMatchDel(&match); } } ajReportSetTailS(report,tailstr); ajReportWrite(report, tab, sequence); ajReportDel(&report); ajFeattableDel(&tab); ajStrDel(&temp); ajStrDel(®exp); ajStrDel(&savereg); ajStrDel(&str); ajStrDel(&data); ajStrDel(&docdata); ajStrDel(&text); ajStrDel(&redatanew); ajStrDel(&accession); ajSeqDel(&sequence); ajStrDel(&tailstr); ajStrDel(&fthit); ajStrDel(&name); ajStrDel(&tmpstr); ajFeattableDel(&tab); ajFileClose(&inf); embExit(); return 0; }
int main(int argc, char **argv) { AjPFile outf = NULL; AjPSeq sequence = NULL; AjPStr substr = NULL; AjPStr seqstr = NULL; AjPStr revstr = NULL; AjPStr p1; AjPStr p2; PPrimer eric = NULL; PPrimer fred = NULL; PPrimer f; PPrimer r; PPair pair; AjPList forlist = NULL; AjPList revlist = NULL; AjPList pairlist = NULL; AjBool targetrange; AjBool isDNA = ajTrue; AjBool dolist = ajFalse; ajint primerlen = 0; ajint minprimerlen = 0; ajint maxprimerlen = 0; ajint minprodlen = 0; ajint maxprodlen = 0; ajint prodlen = 0; ajint seqlen = 0; ajint stepping_value = 1; ajint targetstart = 0; ajint targetend = 0; ajint limit = 0; ajint limit2 = 0; ajint lastpos = 0; ajint startpos = 0; ajint endpos = 0; ajint begin; ajint end; ajint v1; ajint v2; ajint overlap; float minpmGCcont = 0.; float maxpmGCcont = 0.; float minprodGCcont = 0.; float maxprodGCcont = 0.; float prodTm; float prodGC; ajint i; ajint j; ajint neric=0; ajint nfred=0; ajint npair=0; float minprimerTm = 0.0; float maxprimerTm = 0.0; float saltconc = 0.0; float dnaconc = 0.0; embInit ("prima", argc, argv); substr = ajStrNew(); forlist = ajListNew(); revlist = ajListNew(); pairlist = ajListNew(); p1 = ajStrNew(); p2 = ajStrNew(); sequence = ajAcdGetSeq("sequence"); outf = ajAcdGetOutfile("outfile"); minprimerlen = ajAcdGetInt("minprimerlen"); maxprimerlen = ajAcdGetInt("maxprimerlen"); minpmGCcont = ajAcdGetFloat("minpmGCcont"); maxpmGCcont = ajAcdGetFloat("maxpmGCcont"); minprimerTm = ajAcdGetFloat("mintmprimer"); maxprimerTm = ajAcdGetFloat("maxtmprimer"); minprodlen = ajAcdGetInt("minplen"); maxprodlen = ajAcdGetInt("maxplen"); minprodGCcont = ajAcdGetFloat("minpgccont"); maxprodGCcont = ajAcdGetFloat("maxpgccont"); saltconc = ajAcdGetFloat("saltconc"); dnaconc = ajAcdGetFloat("dnaconc"); targetrange = ajAcdGetToggle("targetrange"); targetstart = ajAcdGetInt("targetstart"); targetend = ajAcdGetInt("targetend"); overlap = ajAcdGetInt("overlap"); dolist = ajAcdGetBoolean("list"); seqstr = ajSeqGetSeqCopyS(sequence); ajStrFmtUpper(&seqstr); begin = ajSeqGetBegin(sequence); end = ajSeqGetEnd(sequence); seqlen = end-begin+1; ajStrAssignSubC(&substr,ajStrGetPtr(seqstr),begin-1,end-1); revstr = ajStrNewC(ajStrGetPtr(substr)); ajSeqstrReverse(&revstr); AJCNEW0(entropy, seqlen); AJCNEW0(enthalpy, seqlen); AJCNEW0(energy, seqlen); /* Initialise Tm calculation arrays */ ajMeltTempSave(ajStrGetPtr(substr),0,seqlen,saltconc,dnaconc,1, &entropy, &enthalpy, &energy); ajFmtPrintF(outf, "\n\nINPUT SUMMARY\n"); ajFmtPrintF(outf, "*************\n\n"); if(targetrange) ajFmtPrintF (outf, "Prima of %s from positions %d to %d bps\n", ajSeqGetNameC(sequence),targetstart, targetend); else ajFmtPrintF(outf, "Prima of %s\n", ajSeqGetNameC(sequence)); ajFmtPrintF(outf, "PRIMER CONSTRAINTS:\n"); ajFmtPrintF (outf, "PRIMA DOES NOT ALLOW PRIMER SEQUENCE AMBIGUITY OR "); ajFmtPrintF(outf,"DUPLICATE PRIMER ENDPOINTS\n"); ajFmtPrintF(outf, "Primer size range is %d-%d\n",minprimerlen,maxprimerlen); ajFmtPrintF(outf, "Primer GC content range is %.2f-%.2f\n",minpmGCcont, maxpmGCcont); ajFmtPrintF(outf,"Primer melting Temp range is %.2f - %.2f C\n", minprimerTm, maxprimerTm); ajFmtPrintF (outf, "PRODUCT CONSTRAINTS:\n"); ajFmtPrintF(outf,"Product GC content range is %.2f-%.2f\n", minprodGCcont, maxprodGCcont); ajFmtPrintF(outf, "Salt concentration is %.2f (mM)\n", saltconc); ajFmtPrintF(outf, "DNA concentration is %.2f (nM)\n", dnaconc); if(targetrange) ajFmtPrintF(outf, "Targeted range to amplify is from %d to %d\n", targetstart,targetend); else { ajFmtPrintF(outf,"Considering all suitable Primer pairs with "); ajFmtPrintF(outf,"Product length ranges %d to %d\n\n\n", minprodlen, maxprodlen); } ajFmtPrintF(outf, "\n\nPRIMER/PRODUCT PAIR CALCULATIONS & OUTPUT\n"); ajFmtPrintF(outf, "*****************************************\n\n"); if(seqlen-minprimerlen < 0) ajFatal("Sequence too short"); if(targetrange) { ajStrAssignSubC(&p1,ajStrGetPtr(substr),targetstart-begin,targetend-begin); prodGC = ajMeltGC(substr,seqlen); prodTm = ajMeltTempProd(prodGC,saltconc,seqlen); if(prodGC<minprodGCcont || prodGC>maxprodGCcont) { ajFmtPrintF(outf, "Product GC content [%.2f] outside acceptable range\n", prodGC); embExitBad(); return 0; } prima_testtarget(substr, revstr, targetstart-begin, targetend-begin, minprimerlen, maxprimerlen, seqlen, minprimerTm, maxprimerTm, minpmGCcont, maxpmGCcont, minprodGCcont, maxprodGCcont, saltconc, dnaconc, pairlist, &npair); } if(!targetrange) { limit = seqlen-minprimerlen-minprodlen+1; lastpos = seqlen-minprodlen; limit2 = maxprodlen-minprodlen; /* Outer loop selects all possible product start points */ for(i=minprimerlen; i<limit; ++i) { startpos = i; ajDebug("Position in sequence %d\n",startpos); endpos = i+minprodlen-1; /* Inner loop selects all possible product lengths */ for(j=0; j<limit2; ++j, ++endpos) { if(endpos>lastpos) break; v1 = endpos-startpos+1; ajStrAssignSubC(&p1,ajStrGetPtr(substr),startpos,endpos); prodGC = ajMeltGC(p1,v1); prodTm = ajMeltTempProd(prodGC,saltconc,v1); if(prodGC<minprodGCcont || prodGC>maxprodGCcont) continue; /* Only accept primers with acceptable Tm and GC */ neric = 0; nfred = 0; prima_testproduct(substr, startpos, endpos, primerlen, minprimerlen, maxprimerlen,minpmGCcont, maxpmGCcont, minprimerTm, maxprimerTm, minprodlen, maxprodlen, prodTm, prodGC, seqlen, &eric,&fred,forlist,revlist,&neric,&nfred, stepping_value, saltconc,dnaconc, isDNA, begin); if(!neric) continue; /* Now reject those primers with self-complementarity */ prima_reject_self(forlist,revlist,&neric,&nfred); if(!neric) continue; /* Reject any primers that could bind elsewhere in the sequence */ prima_test_multi(forlist,revlist,&neric,&nfred,substr,revstr, seqlen); /* Now select the least complementary pair (if any) */ prima_best_primer(forlist, revlist, &neric, &nfred); if(!neric) continue; AJNEW(pair); ajListPop(forlist,(void **)&f); ajListPop(revlist,(void **)&r); pair->f = f; pair->r = r; ++npair; ajListPush(pairlist,(void *)pair); } } } if(!targetrange) { /* Get rid of primer pairs nearby the top scoring ones */ prima_TwoSortscorepos(&pairlist); prima_prune_nearby(pairlist, &npair, maxprimerlen-1); ajListSort(pairlist,prima_PosCompare); prima_check_overlap(pairlist,&npair,overlap); } if(npair) { if(!targetrange) ajFmtPrintF(outf,"%d pairs found\n\n",npair); else ajFmtPrintF(outf, "Closest primer pair to specified product is:\n\n"); if((maxprimerlen<26 && seqlen<999999 && !dolist)) ajFmtPrintF(outf,"\n\t\tForward\t\t\t\t\tReverse\n\n"); } for(i=0;i<npair;++i) { if(!targetrange) ajFmtPrintF(outf,"[%d]\n",i+1); ajListPop(pairlist,(void **)&pair); prodlen = pair->r->start - (pair->f->start + pair->f->primerlen); if((maxprimerlen<26 && seqlen<999999 && !dolist)) { v1 = pair->f->start; v2 = v1 + pair->f->primerlen -1; ajStrAssignSubS(&p1,substr,v1,v2); ajFmtPrintF(outf,"%6d %-25.25s %d\t", v1+begin, ajStrGetPtr(p1), v2+begin); v1 = pair->r->start; v2 = v1 + pair->r->primerlen -1; ajStrAssignSubS(&p2,substr,v1,v2); ajSeqstrReverse(&p2); ajFmtPrintF(outf, "%6d %-25.25s %d\n", v1+begin, ajStrGetPtr(p2), v2+begin); ajFmtPrintF(outf," Tm %.2f C (GC %.2f%%)\t\t ", pair->f->primerTm,pair->f->primGCcont*100.); ajFmtPrintF(outf,"Tm %.2f C (GC %.2f%%)\n", pair->r->primerTm,pair->r->primGCcont*100.); ajFmtPrintF(outf," Length: %-32dLength: %d\n", pair->f->primerlen,pair->r->primerlen); ajFmtPrintF(outf," Tma: %.2f C\t\t\t", ajAnneal(pair->f->primerTm,pair->f->prodTm)); ajFmtPrintF(outf," Tma: %.2f C\n\n\n", ajAnneal(pair->r->primerTm,pair->f->prodTm)); ajFmtPrintF(outf," Product GC: %.2f%%\n", pair->f->prodGC * 100.0); ajFmtPrintF(outf," Product Tm: %.2f C\n", pair->f->prodTm); ajFmtPrintF(outf," Length: %d\n\n\n",prodlen); } else { ajFmtPrintF(outf," Product from %d to %d\n",pair->f->start+ pair->f->primerlen+begin,pair->r->start-1+begin); ajFmtPrintF(outf," Tm: %.2f C GC: %.2f%%\n", pair->f->prodTm,pair->f->prodGC*(float)100.); ajFmtPrintF(outf," Length: %d\n\n\n",prodlen); v1 = pair->f->start; v2 = v1 + pair->f->primerlen -1; ajStrAssignSubS(&p1,substr,v1,v2); ajFmtPrintF(outf," Forward: 5' %s 3'\n",ajStrGetPtr(p1)); ajFmtPrintF(outf," Start: %d\n",v1+begin); ajFmtPrintF(outf," End: %d\n",v2+begin); ajFmtPrintF(outf," Tm: %.2f C\n", pair->f->primerTm); ajFmtPrintF(outf," GC: %.2f%%\n", pair->f->primGCcont*(float)100.); ajFmtPrintF(outf," Len: %d\n", pair->f->primerlen); ajFmtPrintF(outf," Tma: %.2f C\n\n\n", ajAnneal(pair->f->primerTm,pair->f->prodTm)); v1 = pair->r->start; v2 = v1 + pair->r->primerlen -1; ajStrAssignSubS(&p2,substr,v1,v2); ajSeqstrReverse(&p2); ajStrAssignSubS(&p1,substr,v1,v2); ajFmtPrintF(outf," Reverse: 5' %s 3'\n",ajStrGetPtr(p1)); ajFmtPrintF(outf," Start: %d\n",v1+begin); ajFmtPrintF(outf," End: %d\n",v2+begin); ajFmtPrintF(outf," Tm: %.2f C\n", pair->r->primerTm); ajFmtPrintF(outf," GC: %.2f%%\n", pair->r->primGCcont*(float)100.); ajFmtPrintF(outf," Len: %d\n", pair->r->primerlen); ajFmtPrintF(outf," Tma: %.2f C\n\n\n", ajAnneal(pair->r->primerTm,pair->f->prodTm)); } prima_PrimerDel(&pair->f); prima_PrimerDel(&pair->r); AJFREE(pair); } ajStrDel(&seqstr); ajStrDel(&revstr); ajStrDel(&substr); ajStrDel(&p1); ajStrDel(&p2); ajListFree(&forlist); ajListFree(&revlist); ajListFree(&pairlist); ajFileClose(&outf); ajSeqDel(&sequence); AJFREE(entropy); AJFREE(enthalpy); AJFREE(energy); embExit(); return 0; }
int main(int argc, char **argv) { /* Global details */ AjBool explain_flag; AjBool file_flag; AjPStr* task; AjBool do_primer; AjBool do_hybrid; ajint num_return; ajint first_base_index; /* "Sequence" Input Tags */ AjPSeqall sequence; AjPRange included_region; AjPRange target; AjPRange excluded_region; AjPStr left_input; AjPStr right_input; /* Primer details */ AjBool pick_anyway; AjPFile mispriming_library; float max_mispriming; float pair_max_mispriming; ajint gc_clamp; ajint opt_size; ajint min_size; ajint max_size; float opt_tm; float min_tm; float max_tm; float max_diff_tm; float opt_gc_percent; float min_gc; float max_gc; float salt_conc; float dna_conc; ajint num_ns_accepted; float self_any; float self_end; ajint max_poly_x; /* Sequence Quality. These are not (yet) implemented */ /* AjPFile sequence_quality; ajint min_quality; ajint min_end_quality; ajint quality_range_min; ajint quality_range_max; */ /* Product details */ ajint product_opt_size; AjPRange product_size_range; float product_opt_tm; float product_min_tm; float product_max_tm; /* Objective Function Penalty Weights for Primers */ float max_end_stability; /* these are not (yet) implemented */ /* float inside_penalty; float outside_penalty; */ /* Primer penalties */ /* these are not (yet) implemented */ /* Internal Oligo "Sequence" Input Tags */ AjPRange internal_oligo_excluded_region; /* Internal Oligo "Global" Input Tags */ AjPStr internal_oligo_input; ajint internal_oligo_opt_size; ajint internal_oligo_min_size; ajint internal_oligo_max_size; float internal_oligo_opt_tm; float internal_oligo_min_tm; float internal_oligo_max_tm; float internal_oligo_opt_gc_percent; float internal_oligo_min_gc; float internal_oligo_max_gc; float internal_oligo_salt_conc; float internal_oligo_dna_conc; float internal_oligo_self_any; float internal_oligo_self_end; ajint internal_oligo_max_poly_x; AjPFile internal_oligo_mishyb_library; float internal_oligo_max_mishyb; /* ajint internal_oligo_min_quality; */ /* Internal Oligo penalties */ /* these are not (yet) implemented */ /* EMBOSS-wrapper-specific stuff */ AjPFile outfile; /* other variables */ AjPStr result = NULL; AjPStr strand = NULL; AjPStr substr = NULL; AjPSeq seq = NULL; ajint begin = 0; ajint end; FILE* stream; AjPStr taskstr = NULL; const AjPStr program = NULL; /* pipe variables */ int *pipeto; /* pipe to feed the exec'ed program input */ int *pipefrom; /* pipe to get the exec'ed program output */ embInit("eprimer3", argc, argv); /* Global details */ explain_flag = ajAcdGetBoolean("explainflag"); file_flag = ajAcdGetBoolean("fileflag"); task = ajAcdGetList("task"); do_primer = ajAcdGetToggle("primer"); do_hybrid = ajAcdGetToggle("hybridprobe"); num_return = ajAcdGetInt("numreturn"); first_base_index = ajAcdGetInt("firstbaseindex"); /* "Sequence" Input Tags */ sequence = ajAcdGetSeqall("sequence"); included_region = ajAcdGetRange("includedregion"); target = ajAcdGetRange("targetregion"); excluded_region = ajAcdGetRange("excludedregion"); left_input = ajAcdGetString("forwardinput"); right_input = ajAcdGetString("reverseinput"); /* Primer details */ pick_anyway = ajAcdGetBoolean("pickanyway"); mispriming_library = ajAcdGetInfile("mispriminglibraryfile"); max_mispriming = ajAcdGetFloat("maxmispriming"); pair_max_mispriming = ajAcdGetFloat("pairmaxmispriming"); gc_clamp = ajAcdGetInt("gcclamp"); opt_size = ajAcdGetInt("osize"); min_size = ajAcdGetInt("minsize"); max_size = ajAcdGetInt("maxsize"); opt_tm = ajAcdGetFloat("otm"); min_tm = ajAcdGetFloat("mintm"); max_tm = ajAcdGetFloat("maxtm"); max_diff_tm = ajAcdGetFloat("maxdifftm"); opt_gc_percent = ajAcdGetFloat("ogcpercent"); min_gc = ajAcdGetFloat("mingc"); max_gc = ajAcdGetFloat("maxgc"); salt_conc = ajAcdGetFloat("saltconc"); dna_conc = ajAcdGetFloat("dnaconc"); num_ns_accepted = ajAcdGetInt("numnsaccepted"); self_any = ajAcdGetFloat("selfany"); self_end = ajAcdGetFloat("selfend"); max_poly_x = ajAcdGetInt("maxpolyx"); AJCNEW0(pipeto,2); AJCNEW0(pipefrom,2); /* Sequence Quality */ /* these are not (yet) implemented */ /* sequence_quality = ajAcdGetInfile("sequencequality"); min_quality = ajAcdGetInt("minquality"); min_end_quality = ajAcdGetInt("minendquality"); quality_range_min = ajAcdGetInt("qualityrangemin"); quality_range_max = ajAcdGetInt("qualityrangemax"); */ /* Product details */ product_opt_size = ajAcdGetInt("psizeopt"); product_size_range = ajAcdGetRange("prange"); product_opt_tm = ajAcdGetFloat("ptmopt"); product_min_tm = ajAcdGetFloat("ptmmin"); product_max_tm = ajAcdGetFloat("ptmmax"); /* Objective Function Penalty Weights for Primers */ max_end_stability = ajAcdGetFloat("maxendstability"); /* these are not (yet) implemented */ /* inside_penalty = ajAcdGetFloat("insidepenalty"); outside_penalty = ajAcdGetFloat("outsidepenalty"); */ /* Primer penalties */ /* these are not (yet) implemented */ /* Internal Oligo "Sequence" Input Tags */ internal_oligo_excluded_region = ajAcdGetRange("oexcludedregion"); internal_oligo_input = ajAcdGetString("oligoinput"); /* Internal Oligo "Global" Input Tags */ internal_oligo_opt_size = ajAcdGetInt("osizeopt"); internal_oligo_min_size = ajAcdGetInt("ominsize"); internal_oligo_max_size = ajAcdGetInt("omaxsize"); internal_oligo_opt_tm = ajAcdGetFloat("otmopt"); internal_oligo_min_tm = ajAcdGetFloat("otmmin"); internal_oligo_max_tm = ajAcdGetFloat("otmmax"); internal_oligo_opt_gc_percent = ajAcdGetFloat("ogcopt"); internal_oligo_min_gc = ajAcdGetFloat("ogcmin"); internal_oligo_max_gc = ajAcdGetFloat("ogcmax"); internal_oligo_salt_conc = ajAcdGetFloat("osaltconc"); internal_oligo_dna_conc = ajAcdGetFloat("odnaconc"); internal_oligo_self_any = ajAcdGetFloat("oanyself"); internal_oligo_self_end = ajAcdGetFloat("oendself"); internal_oligo_max_poly_x = ajAcdGetInt("opolyxmax"); internal_oligo_mishyb_library = ajAcdGetInfile("mishyblibraryfile"); internal_oligo_max_mishyb = ajAcdGetFloat("omishybmax"); /* internal_oligo_min_quality = ajAcdGetInt("oligominquality"); */ /* Internal Oligo penalties */ /* these are not (yet) implemented */ /* EMBOSS-wrapper-specific stuff */ outfile = ajAcdGetOutfile("outfile"); ajStrRemoveWhite(&left_input); ajStrRemoveWhite(&right_input); /* ** OK - we will now try to do a separate fork-exec for each sequence. */ result = ajStrNew(); while(ajSeqallNext(sequence, &seq)) { program = ajAcdGetpathC("primer3_core"); if(!ajSysExecRedirectC(ajStrGetPtr(program),&pipeto,&pipefrom)) ajFatal("eprimer3: Could not exec primer3_core"); stream = eprimer3_start_write(pipeto[1]); /* send primer3 Primer "Global" parameters */ eprimer3_send_bool(stream, "PRIMER_EXPLAIN_FLAG", explain_flag); eprimer3_send_bool(stream, "PRIMER_FILE_FLAG", file_flag); if(do_hybrid) { if(!ajStrCmpC(task[0], "1")) ajStrAssignC(&taskstr, "pick_pcr_primers_and_hyb_probe"); else if(!ajStrCmpC(task[0], "2")) ajStrAssignC(&taskstr, "pick_left_only"); else if(!ajStrCmpC(task[0], "3")) ajStrAssignC(&taskstr, "pick_right_only"); else if(!ajStrCmpC(task[0], "4")) ajStrAssignC(&taskstr, "pick_hyb_probe_only"); if (!do_primer) ajStrAssignC(&taskstr, "pick_hyb_probe_only"); } else { if(!ajStrCmpC(task[0], "1")) ajStrAssignC(&taskstr, "pick_pcr_primers"); else if(!ajStrCmpC(task[0], "2")) ajStrAssignC(&taskstr, "pick_left_only"); else if(!ajStrCmpC(task[0], "3")) ajStrAssignC(&taskstr, "pick_right_only"); else if(!ajStrCmpC(task[0], "4")) ajStrAssignC(&taskstr, "pick_hyb_probe_only"); } eprimer3_send_string(stream, "PRIMER_TASK", taskstr); eprimer3_send_int(stream, "PRIMER_NUM_RETURN", num_return); eprimer3_send_int(stream, "PRIMER_FIRST_BASE_INDEX", first_base_index); eprimer3_send_bool(stream, "PRIMER_PICK_ANYWAY", pick_anyway); /* mispriming library may not have been specified */ if(mispriming_library) eprimer3_send_stringC(stream, "PRIMER_MISPRIMING_LIBRARY", ajFileGetPrintnameC(mispriming_library)); eprimer3_send_float(stream, "PRIMER_MAX_MISPRIMING", max_mispriming); eprimer3_send_float(stream, "PRIMER_PAIR_MAX_MISPRIMING", pair_max_mispriming); eprimer3_send_int(stream, "PRIMER_GC_CLAMP", gc_clamp); eprimer3_send_int(stream, "PRIMER_OPT_SIZE", opt_size); eprimer3_send_int(stream, "PRIMER_MIN_SIZE", min_size); eprimer3_send_int(stream, "PRIMER_MAX_SIZE", max_size); eprimer3_send_float(stream, "PRIMER_OPT_TM", opt_tm); eprimer3_send_float(stream, "PRIMER_MIN_TM", min_tm); eprimer3_send_float(stream, "PRIMER_MAX_TM", max_tm); eprimer3_send_float(stream, "PRIMER_MAX_DIFF_TM", max_diff_tm); eprimer3_send_float(stream, "PRIMER_OPT_GC_PERCENT", opt_gc_percent); eprimer3_send_float(stream, "PRIMER_MIN_GC", min_gc); eprimer3_send_float(stream, "PRIMER_MAX_GC", max_gc); eprimer3_send_float(stream, "PRIMER_SALT_CONC", salt_conc); eprimer3_send_float(stream, "PRIMER_DNA_CONC", dna_conc); eprimer3_send_int(stream, "PRIMER_NUM_NS_ACCEPTED", num_ns_accepted); eprimer3_send_float(stream, "PRIMER_SELF_ANY", self_any); eprimer3_send_float(stream, "PRIMER_SELF_END", self_end); eprimer3_send_int(stream, "PRIMER_MAX_POLY_X", max_poly_x); eprimer3_send_int(stream, "PRIMER_PRODUCT_OPT_SIZE", product_opt_size); eprimer3_send_range2(stream, "PRIMER_PRODUCT_SIZE_RANGE", product_size_range); eprimer3_send_float(stream, "PRIMER_PRODUCT_OPT_TM", product_opt_tm); eprimer3_send_float(stream, "PRIMER_PRODUCT_MIN_TM", product_min_tm); eprimer3_send_float(stream, "PRIMER_PRODUCT_MAX_TM", product_max_tm); eprimer3_send_float(stream, "PRIMER_MAX_END_STABILITY", max_end_stability); /* send primer3 Internal Oligo "Global" parameters */ eprimer3_send_int(stream, "PRIMER_INTERNAL_OLIGO_OPT_SIZE", internal_oligo_opt_size); eprimer3_send_int(stream, "PRIMER_INTERNAL_OLIGO_MIN_SIZE", internal_oligo_min_size); eprimer3_send_int(stream, "PRIMER_INTERNAL_OLIGO_MAX_SIZE", internal_oligo_max_size); eprimer3_send_float(stream, "PRIMER_INTERNAL_OLIGO_OPT_TM", internal_oligo_opt_tm); eprimer3_send_float(stream, "PRIMER_INTERNAL_OLIGO_MIN_TM", internal_oligo_min_tm); eprimer3_send_float(stream, "PRIMER_INTERNAL_OLIGO_MAX_TM", internal_oligo_max_tm); eprimer3_send_float(stream, "PRIMER_INTERNAL_OLIGO_OPT_GC_PERCENT", internal_oligo_opt_gc_percent); eprimer3_send_float(stream, "PRIMER_INTERNAL_OLIGO_MIN_GC", internal_oligo_min_gc); eprimer3_send_float(stream, "PRIMER_INTERNAL_OLIGO_MAX_GC", internal_oligo_max_gc); eprimer3_send_float(stream, "PRIMER_INTERNAL_OLIGO_SALT_CONC", internal_oligo_salt_conc); eprimer3_send_float(stream, "PRIMER_INTERNAL_OLIGO_DNA_CONC", internal_oligo_dna_conc); eprimer3_send_float(stream, "PRIMER_INTERNAL_OLIGO_SELF_ANY", internal_oligo_self_any); eprimer3_send_float(stream, "PRIMER_INTERNAL_OLIGO_SELF_END", internal_oligo_self_end); eprimer3_send_int(stream, "PRIMER_INTERNAL_OLIGO_MAX_POLY_X", internal_oligo_max_poly_x); /* ** internal oligo mishybridising library may not have been ** specified */ if(internal_oligo_mishyb_library) eprimer3_send_stringC(stream, "PRIMER_INTERNAL_OLIGO_MISHYB_LIBRARY", ajFileGetPrintnameC(internal_oligo_mishyb_library)); eprimer3_send_float(stream, "PRIMER_INTERNAL_OLIGO_MAX_MISHYB", internal_oligo_max_mishyb); /* ** Start sequence-specific stuff */ begin = ajSeqallGetseqBegin(sequence) - 1; end = ajSeqallGetseqEnd(sequence) - 1; strand = ajSeqGetSeqCopyS(seq); ajStrFmtUpper(&strand); ajStrAssignSubC(&substr,ajStrGetPtr(strand), begin, end); /* send flags to turn on using optimal product size */ eprimer3_send_float(stream, "PRIMER_PAIR_WT_PRODUCT_SIZE_GT", (float)0.05); eprimer3_send_float(stream, "PRIMER_PAIR_WT_PRODUCT_SIZE_LT", (float)0.05); /* send primer3 Primer "Sequence" parameters */ eprimer3_send_string(stream, "SEQUENCE", substr); /* if no ID name, use the USA */ if(ajStrMatchC(ajSeqGetNameS(seq),"")) eprimer3_send_string(stream, "PRIMER_SEQUENCE_ID", ajSeqGetUsaS(seq)); else eprimer3_send_string(stream, "PRIMER_SEQUENCE_ID", ajSeqGetNameS(seq)); eprimer3_send_range(stream, "INCLUDED_REGION", included_region, begin); eprimer3_send_range(stream, "TARGET", target, begin); eprimer3_send_range(stream, "EXCLUDED_REGION", excluded_region, begin); eprimer3_send_string(stream, "PRIMER_LEFT_INPUT", left_input); eprimer3_send_string(stream, "PRIMER_RIGHT_INPUT", right_input); /* send primer3 Internal Oligo "Sequence" parameters */ eprimer3_send_range(stream, "PRIMER_INTERNAL_OLIGO_EXCLUDED_REGION", internal_oligo_excluded_region, begin); eprimer3_send_string(stream, "PRIMER_INTERNAL_OLIGO_INPUT", internal_oligo_input); /* end the primer3 input sequence record with a '=' */ eprimer3_send_end(stream); /* and close the ouput pipe stream */ eprimer3_end_write(stream); /* read the primer3 output */ eprimer3_read(pipefrom[0], &result); eprimer3_report(outfile, result, num_return, begin); ajStrSetClear(&result); #ifndef WIN32 close(pipeto[1]); close(pipefrom[0]); #endif } /* end of sequence loop */ ajStrDel(&result); ajSeqDel(&seq); ajStrDel(&strand); ajStrDel(&substr); ajFileClose(&outfile); ajStrDel(&taskstr); ajStrDelarray(&task); ajSeqallDel(&sequence); ajSeqDel(&seq); ajRangeDel(&included_region); ajRangeDel(&target); ajRangeDel(&excluded_region); ajRangeDel(&product_size_range); ajRangeDel(&internal_oligo_excluded_region); ajStrDel(&left_input); ajStrDel(&right_input); ajStrDel(&internal_oligo_input); AJFREE(pipeto); AJFREE(pipefrom); ajFileClose(&mispriming_library); embExit(); return 0; }
int main(int argc, char **argv) { AjPSeqall seqall; AjPSeq seq = NULL; AjPFile outf = NULL; ajint begin; ajint end; ajuint emin; ajuint emax; AjPFile mfile = NULL; EmbPMatPrints s = NULL; AjPList l = NULL; AjPStr strand = NULL; AjPStr substr = NULL; AjPStr name = NULL; AjBool all; AjBool ordered; ajint hits; ajint nmotifs; embInit("pscan", argc, argv); seqall = ajAcdGetSeqall("sequence"); outf = ajAcdGetOutfile("outfile"); emin = ajAcdGetInt("emin"); emax = ajAcdGetInt("emax"); substr = ajStrNew(); name = ajStrNew(); all = ordered = ajTrue; while(ajSeqallNext(seqall, &seq)) { begin = ajSeqallGetseqBegin(seqall); end = ajSeqallGetseqEnd(seqall); ajStrAssignC(&name,ajSeqGetNameC(seq)); strand = ajSeqGetSeqCopyS(seq); ajStrAssignSubC(&substr,ajStrGetPtr(strand),begin-1,end-1); nmotifs = 0; ajDebug("pscan sequence '%S'\n", ajSeqGetNameS(seq)); embMatPrintsInit(&mfile); ajDebug("pscan prints file '%F'\n", mfile); l = ajListNew(); while((s = embMatProtReadInt(mfile))) { ajDebug("pscan file '%F' read\n", mfile); if(s->n >= emin && s->n <= emax) { hits=embMatProtScanInt(substr,name,s,&l,&all,&ordered, 1); if(hits) ++nmotifs; } embMatProtDelInt(&s); } pscan_print_hits(outf, l, nmotifs, begin); ajListFree(&l); ajStrDel(&strand); ajFileClose(&mfile); } ajStrDel(&substr); ajStrDel(&name); ajSeqallDel(&seqall); ajSeqDel(&seq); ajFileClose(&outf); embExit(); return 0; }
int main(int argc, char **argv) { AjPSeq seq = NULL; AjPStr strand = NULL; AjPStr substr = NULL; AjPStr squares = NULL; AjPStr diamonds = NULL; AjPStr octags = NULL; AjBool amphipathic; AjPStr txt = NULL; AjPGraph graph = NULL; ajint begin; ajint end; ajint lc; ajint i; ajint j; ajint r; ajint count; ajint pstart; ajint pstop; float xmin = 0.0; float xmax = 150.0; float ymin = 0.0; float ymax = 112.5; float xstart; float ystart; float ch = (float)1.8; float xinc; float yinc; AjPStr fstr = NULL; float x; float y; embInit("pepnet", argc, argv); seq = ajAcdGetSeq("sequence"); graph = ajAcdGetGraph("graph"); octags = ajAcdGetString("octags"); squares = ajAcdGetString("squares"); diamonds = ajAcdGetString("diamonds"); amphipathic = ajAcdGetToggle("amphipathic"); ajStrFmtUpper(&octags); ajStrFmtUpper(&squares); ajStrFmtUpper(&diamonds); if(amphipathic) { ajStrAssignC(&squares,"ACFGILMVWY"); ajStrAssignC(&diamonds,""); ajStrAssignC(&octags,""); } substr = ajStrNew(); txt = ajStrNew(); fstr = ajStrNew(); begin = ajSeqGetBegin(seq); end = ajSeqGetEnd(seq); strand = ajSeqGetSeqCopyS(seq); ajStrFmtUpper(&strand); ajStrAssignSubC(&substr,ajStrGetPtr(strand),begin-1,end-1); ajGraphAppendTitleS(graph, ajSeqGetUsaS(seq)); ajGraphOpenWin(graph, xmin,xmax,ymin,ymax); for(count=begin-1,r=0;count<end;count+=231) { if (count > begin) ajGraphNewpage(graph, ajFalse); pstart=count; pstop = AJMIN(end-1, count+230); ajGraphicsSetCharscale(0.75); xstart = 145.0; ystart = 80.0; yinc = ch * (float)2.5; xinc = yinc / (float)2.5; x = xstart; for(i=pstart;i<=pstop;i+=7) { lc = i; if(x < 10.0*xinc) { x = xstart; ystart -= (float)7.5*yinc; } y=ystart; ajFmtPrintS(&txt,"%d",i+1); ajGraphicsSetFgcolour(RED); ajGraphicsDrawposTextJustify(x-xinc,y-yinc-1,ajStrGetPtr(txt),0.5); for(j=0;j<4;++j) { x -= xinc; y += yinc; if(lc <= pstop) pepnet_plotresidue(*(ajStrGetPtr(substr)+r),x,y, ajStrGetPtr(squares),ajStrGetPtr(octags), ajStrGetPtr(diamonds)); ++r; ++lc; } y=ystart+yinc/(float)2.0; for(j=4;j<7;++j) { x -= xinc; y += yinc; if(lc <= pstop) pepnet_plotresidue(*(ajStrGetPtr(substr)+r),x,y, ajStrGetPtr(squares),ajStrGetPtr(octags), ajStrGetPtr(diamonds)); ++r; ++lc; } } } ajGraphicsClose(); ajGraphxyDel(&graph); ajStrDel(&strand); ajStrDel(&fstr); ajSeqDel(&seq); ajStrDel(&substr); ajStrDel(&squares); ajStrDel(&diamonds); ajStrDel(&octags); ajStrDel(&txt); embExit(); return 0; }
int main(int argc, char **argv) { AjPSeq seq = NULL; AjPStr strand = NULL; AjPStr substr = NULL; AjPStr squares = NULL; AjPStr diamonds = NULL; AjPStr octags = NULL; AjBool wheel; AjBool amphipathic; AjPGraph graph=0; AjBool first; AjBool startloop; ajint begin; ajint end; ajint len; ajint steps; ajint turns; ajint lc; ajint i; ajint j; ajint k; float xmin = (float) -1.0; float xmax = (float) 1.0; float ymin = (float) -0.75; float ymax = (float) 0.75; float minresplot = (float) 36.0; float resgap = (float) 0.0533; float wheelgap = (float) 0.00; float nresgap = (float) 0.08; float angle; float oldangle; float ang; float radius; float wradius; float xx1; float xx2; float yy1; float yy2; embInit("pepwheel", argc, argv); seq = ajAcdGetSeq("sequence"); steps = ajAcdGetInt("steps"); turns = ajAcdGetInt("turns"); graph = ajAcdGetGraph("graph"); octags = ajAcdGetString("octags"); squares = ajAcdGetString("squares"); diamonds = ajAcdGetString("diamonds"); wheel = ajAcdGetBoolean("wheel"); amphipathic = ajAcdGetToggle("amphipathic"); ajStrFmtUpper(&octags); ajStrFmtUpper(&squares); ajStrFmtUpper(&diamonds); if(amphipathic) { ajStrAssignC(&squares,"ACFGILMVWY"); ajStrAssignC(&diamonds,""); ajStrAssignC(&octags,""); } substr = ajStrNew(); begin = ajSeqGetBegin(seq); end = ajSeqGetEnd(seq); ajDebug("begin: %d end: %d\n", begin, end); strand = ajSeqGetSeqCopyS(seq); ajStrFmtUpper(&strand); ajStrAssignSubC(&substr,ajStrGetPtr(strand),begin-1,end-1); len = ajStrGetLen(substr); ajGraphAppendTitleS(graph, ajSeqGetUsaS(seq)); ajGraphOpenWin(graph,xmin,xmax,ymin,ymax); ajGraphicsSetFgcolour(AJB_BLACK); ang = ((float)360.0 / (float)steps) * (float)turns; first = ajTrue; angle = (float) 90.0 + ang; if(end-begin > (ajint)minresplot) wradius = (float) 0.2; else wradius = (float) 0.40; for(i=0,lc=0,radius=wradius+wheelgap;i<len;i+=steps) { wradius += wheelgap; startloop = ajTrue; k = AJMIN(i+steps, end); for(j=i;j<k;++j) { oldangle = angle; angle = oldangle-ang; if(first) startloop = first = ajFalse; else { if(startloop) { if(wheel) { ajCvtPolToRec(wradius-wheelgap,oldangle,&xx1,&yy1); ajCvtPolToRec(wradius,angle,&xx2,&yy2); ajGraphicsDrawposLine(xx1,yy1,xx2,yy2); } startloop=ajFalse; } else if(wheel) { ajCvtPolToRec(wradius,oldangle,&xx1,&yy1); ajCvtPolToRec(wradius,angle,&xx2,&yy2); ajGraphicsDrawposLine(xx1,yy1,xx2,yy2); } } pepwheel_plotresidue(*(ajStrGetPtr(substr)+lc),radius+resgap,angle, ajStrGetPtr(squares),ajStrGetPtr(octags), ajStrGetPtr(diamonds), xmin,xmax,ymin,ymax); ++lc; if(lc==len) break; } radius += nresgap; } ajGraphicsClose(); ajGraphxyDel(&graph); ajStrDel(&strand); ajStrDel(&substr); ajSeqDel(&seq); ajStrDel(&squares); ajStrDel(&diamonds); ajStrDel(&octags); embExit(); return 0; }
int main(int argc, char **argv) { AjPSeqall seqall; AjPSeq seq = NULL; AjPFile inf = NULL; AjPStr strand = NULL; AjPStr substr = NULL; AjPStr name = NULL; AjPStr mname = NULL; AjPStr tname = NULL; AjPStr pname = NULL; AjPStr line = NULL; AjPStr cons = NULL; AjPStr m = NULL; AjPStr n = NULL; AjPAlign align= NULL; /* JISON, replaces AjPOutfile outf */ ajint type; ajint begin; ajint end; ajulong len; ajint i; ajint j; float **fmatrix=NULL; ajint mlen; float maxfs; ajint thresh; float gapopen; float gapextend; float opencoeff; float extendcoeff; const char *p; ajulong maxarr = 1000; ajulong alen; float *path; ajint *compass; size_t stlen; embInit("prophet", argc, argv); seqall = ajAcdGetSeqall("sequence"); inf = ajAcdGetInfile("infile"); opencoeff = ajAcdGetFloat("gapopen"); extendcoeff = ajAcdGetFloat("gapextend"); align = ajAcdGetAlign("outfile"); /*JISON replacing outfile */ opencoeff = ajRoundFloat(opencoeff, 8); extendcoeff = ajRoundFloat(extendcoeff, 8); substr = ajStrNew(); name = ajStrNew(); mname = ajStrNew(); tname = ajStrNew(); line = ajStrNew(); m = ajStrNewC(""); n = ajStrNewC(""); type = prophet_getType(inf,&tname); if(!type) ajFatal("Unrecognised profile/matrix file format"); prophet_read_profile(inf,&pname,&mname,&mlen,&gapopen,&gapextend,&thresh, &maxfs, &cons); ajAlignSetMatrixName(align, mname); AJCNEW(fmatrix, mlen); for(i=0;i<mlen;++i) { AJCNEW(fmatrix[i], AZ); if(!ajReadlineTrim(inf,&line)) ajFatal("Missing matrix line"); p = ajStrGetPtr(line); p = ajSysFuncStrtok(p," \t"); for(j=0;j<AZ;++j) { sscanf(p,"%f",&fmatrix[i][j]); p = ajSysFuncStrtok(NULL," \t"); } } AJCNEW(path, maxarr); AJCNEW(compass, maxarr); while(ajSeqallNext(seqall, &seq)) { begin = ajSeqallGetseqBegin(seqall); end = ajSeqallGetseqEnd(seqall); ajStrAssignC(&name,ajSeqGetNameC(seq)); strand = ajSeqGetSeqCopyS(seq); ajStrAssignSubC(&substr,ajStrGetPtr(strand),begin-1,end-1); len = ajStrGetLen(substr); if(len > (ULONG_MAX/(ajulong)(mlen+1))) ajFatal("Sequences too big. Try 'supermatcher'"); alen = len*mlen; if(alen>maxarr) { stlen = (size_t) alen; AJCRESIZE(path,stlen); AJCRESIZE(compass,stlen); maxarr=alen; } ajStrAssignC(&m,""); ajStrAssignC(&n,""); /* JISON used to be prophet_scan_profile(substr,pname,name,mlen,fmatrix, outf,cons,opencoeff, extendcoeff,path,compass,&m,&n,len); */ /* JISON new call and reset align */ prophet_scan_profile(substr,name,pname,mlen,fmatrix, align,cons,opencoeff, extendcoeff,path,compass,&m,&n,(ajint)len); ajAlignReset(align); ajStrDel(&strand); } for(i=0;i<mlen;++i) AJFREE (fmatrix[i]); AJFREE (fmatrix); AJFREE(path); AJFREE(compass); ajStrDel(&line); ajStrDel(&cons); ajStrDel(&name); ajStrDel(&pname); ajStrDel(&mname); ajStrDel(&tname); ajStrDel(&substr); ajStrDel(&m); ajStrDel(&n); ajSeqDel(&seq); ajFileClose(&inf); ajAlignClose(align); ajAlignDel(&align); ajSeqallDel(&seqall); embExit(); return 0; }
int main(int argc, char **argv) { AjPSeqall seqall; AjPSeq seq = NULL; AjPFile outf = NULL; AjPStr strand = NULL; AjPStr substr = NULL; AjPFeattabOut featout; AjPFeattable feattable=NULL; ajint begin; ajint end; ajint len; ajint score; embInit("cpgreport",argc,argv); seqall = ajAcdGetSeqall("sequence"); score = ajAcdGetInt("score"); outf = ajAcdGetOutfile("outfile"); featout = ajAcdGetFeatout("outfeat"); substr = ajStrNew(); while(ajSeqallNext(seqall, &seq)) { if (!feattable) feattable = ajFeattableNewDna(ajSeqGetNameS(seq)); begin = ajSeqallGetseqBegin(seqall); end = ajSeqallGetseqEnd(seqall); strand = ajSeqGetSeqCopyS(seq); ajStrFmtUpper(&strand); ajStrAssignSubC(&substr,ajStrGetPtr(strand),begin-1,end-1); len=ajStrGetLen(substr); ajFmtPrintF(outf,"\n\nCPGREPORT of %s from %d to %d\n\n", ajSeqGetNameC(seq),begin,begin+len-1); ajFmtPrintF(outf,"Sequence Begin End Score"); ajFmtPrintF(outf," CpG %%CG CG/GC\n"); cpgreport_cpgsearch(outf,0,len,ajStrGetPtr(substr),ajSeqGetNameC(seq), begin,score,feattable); ajStrDel(&strand); } ajSeqDel(&seq); ajStrDel(&substr); ajFileClose(&outf); ajFeatSortByStart(feattable); ajFeattableWrite(featout, feattable); ajFeattableDel(&feattable); ajFeattabOutDel(&featout); ajSeqallDel(&seqall); ajStrDel(&cpgreportSource); ajStrDel(&cpgreportType); embExit(); return 0; }